diff --git a/assembly/pom.xml b/assembly/pom.xml index 0cf047b..94ae35b 100644 --- a/assembly/pom.xml +++ b/assembly/pom.xml @@ -3,12 +3,12 @@ 4.0.0 org.bdgenomics.cannoli - cannoli-parent_2.10 + cannoli-parent-spark2_2.11 0.2.0-SNAPSHOT ../pom.xml - cannoli-assembly_2.10 + cannoli-assembly-spark2_2.11 jar Cannoli_${scala.version.prefix}: Assembly @@ -52,7 +52,7 @@ org.bdgenomics.cannoli - cannoli-cli_${scala.version.prefix} + cannoli-cli-spark2_${scala.version.prefix} compile diff --git a/cli/pom.xml b/cli/pom.xml index 8132655..c2fad3e 100644 --- a/cli/pom.xml +++ b/cli/pom.xml @@ -3,12 +3,12 @@ 4.0.0 org.bdgenomics.cannoli - cannoli-parent_2.10 + cannoli-parent-spark2_2.11 0.2.0-SNAPSHOT ../pom.xml - cannoli-cli_2.10 + cannoli-cli-spark2_2.11 jar Cannoli_${scala.version.prefix}: CLI @@ -74,17 +74,17 @@ org.bdgenomics.adam - adam-cli_${scala.version.prefix} + adam-cli-spark2_${scala.version.prefix} compile org.bdgenomics.cannoli - cannoli-core_${scala.version.prefix} + cannoli-core-spark2_${scala.version.prefix} compile org.bdgenomics.utils - utils-misc_${scala.version.prefix} + utils-misc-spark2_${scala.version.prefix} test-jar test diff --git a/core/pom.xml b/core/pom.xml index 769012a..2acb76f 100644 --- a/core/pom.xml +++ b/core/pom.xml @@ -3,12 +3,12 @@ 4.0.0 org.bdgenomics.cannoli - cannoli-parent_2.10 + cannoli-parent-spark2_2.11 0.2.0-SNAPSHOT ../pom.xml - cannoli-core_2.10 + cannoli-core-spark2_2.11 jar Cannoli_${scala.version.prefix}: Core @@ -49,12 +49,12 @@ org.bdgenomics.adam - adam-core_${scala.version.prefix} + adam-core-spark2_${scala.version.prefix} compile org.bdgenomics.utils - utils-misc_${scala.version.prefix} + utils-misc-spark2_${scala.version.prefix} test-jar test diff --git a/distribution/pom.xml b/distribution/pom.xml index a5f9df7..10cce63 100644 --- a/distribution/pom.xml +++ b/distribution/pom.xml @@ -3,12 +3,12 @@ 4.0.0 org.bdgenomics.cannoli - cannoli-parent_2.10 + cannoli-parent-spark2_2.11 0.2.0-SNAPSHOT ../pom.xml - cannoli-distribution_2.10 + cannoli-distribution-spark2_2.11 pom Cannoli_${scala.version.prefix}: Distribution diff --git a/pom.xml b/pom.xml index 1cf4211..6a55585 100644 --- a/pom.xml +++ b/pom.xml @@ -8,7 +8,7 @@ org.bdgenomics.cannoli - cannoli-parent_2.10 + cannoli-parent-spark2_2.11 0.2.0-SNAPSHOT pom Cannoli_${scala.version.prefix} @@ -17,10 +17,10 @@ 2017 - 0.23.0 - 2.10.6 - 2.10 - 1.6.3 + 0.24.0-SNAPSHOT + 2.11.12 + 2.11 + 2.2.1 UTF-8 UTF-8 [3.1.1,) @@ -349,27 +349,27 @@ org.bdgenomics.adam - adam-core_${scala.version.prefix} + adam-core-spark2_${scala.version.prefix} ${adam.version} org.bdgenomics.adam - adam-cli_${scala.version.prefix} + adam-cli-spark2_${scala.version.prefix} ${adam.version} org.bdgenomics.cannoli - cannoli-core_${scala.version.prefix} + cannoli-core-spark2_${scala.version.prefix} ${project.version} org.bdgenomics.cannoli - cannoli-cli_${scala.version.prefix} + cannoli-cli-spark2_${scala.version.prefix} ${project.version} org.bdgenomics.utils - utils-misc_${scala.version.prefix} + utils-misc-spark2_${scala.version.prefix} ${utils.version} test-jar diff --git a/scripts/jenkins-test b/scripts/jenkins-test index 24703bf..07a57e1 100755 --- a/scripts/jenkins-test +++ b/scripts/jenkins-test @@ -37,61 +37,6 @@ then exit 1 fi -# this next line is supposed to fail -set +e - -echo "Rewriting POM.xml files to Scala 2.10 and Spark 1 should error..." -./scripts/move_to_spark_1.sh -if [[ $? == 0 ]]; -then - echo "Running move_to_spark_1.sh when POMs are set up for Spark 1 should fail, but error code was 0 (success)." - exit 1 -fi - -./scripts/move_to_scala_2.10.sh -if [[ $? == 0 ]]; -then - echo "Running move_to_scala_2.10.sh when POMs are set up for Scala 2.10 should fail, but error code was 0 (success)." - exit 1 -fi - -set -e - -# are we testing for spark 2.0.0? if so, we need to rewrite our poms first -if [ ${SPARK_VERSION} == 2.0.0 ]; -then - - echo "Rewriting POM.xml files for Spark 2." - ./scripts/move_to_spark_2.sh - - # shouldn't be able to move to spark 2 twice - set +e - ./scripts/move_to_spark_2.sh - if [[ $? == 0 ]]; - then - echo "We have already moved to Spark 2, so running move_to_spark_2.sh a second time should fail, but error code was 0 (success)." - exit 1 - fi - set -e -fi - -# are we testing for scala 2.11? if so, we need to rewrite our poms to 2.11 first -if [ ${SCALAVER} == 2.11 ]; -then - echo "Rewriting POM.xml files for Scala 2.11." - ./scripts/move_to_scala_2.11.sh - - # shouldn't be able to move to scala 2.11 twice - set +e - ./scripts/move_to_scala_2.11.sh - if [[ $? == 0 ]]; - then - echo "We have already moved to Scala 2.11, so running move_to_scala_2.11.sh a second time should fail, but error code was 0 (success)." - exit 1 - fi - set -e -fi - # print versions echo "Testing CANNOLI version ${VERSION} on Spark ${SPARK_VERSION} and Hadoop ${HADOOP_VERSION}" @@ -128,20 +73,6 @@ set -x -v find ${CANNOLI_MVN_TMP_DIR} rm -rf ${CANNOLI_MVN_TMP_DIR} -# and move our poms back to their original values -# this will allow us to pass our porcelain test at the end -if [ ${SPARK_VERSION} == 2.0.0 ]; -then - - echo "Rewriting POM.xml files back to Spark 1." - ./scripts/move_to_spark_1.sh -fi -if [ ${SCALAVER} == 2.11 ]; -then - echo "Rewriting POM.xml files back to Scala 2.10." - ./scripts/move_to_scala_2.10.sh -fi - find . -name pom.xml \ -exec sed -i.bak \ -e "s:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=${CANNOLI_MVN_TMP_DIR}:sun.io.serialization.extendedDebugInfo=true:g" \ diff --git a/scripts/move_to_scala_2.10.sh b/scripts/move_to_scala_2.10.sh deleted file mode 100755 index e3ac681..0000000 --- a/scripts/move_to_scala_2.10.sh +++ /dev/null @@ -1,18 +0,0 @@ -#!/bin/bash - -set +x - -grep "" pom.xml | grep -q 2.10 -if [[ $? == 0 ]]; -then - echo "Scala version is already set to 2.10 (Scala artifacts have _2.10 version suffix in artifact name)." - echo "Cowardly refusing to move to Scala 2.10 a second time..." - - exit 1 -fi - -find . -name "pom.xml" -exec sed -e "s/2.11.8/2.10.6/g" \ - -e "/bdg-utils.version/! s/2.11/2.10/g" -i.2.10.bak \ - -e "/no Scala/ s/Scala 2.10/Scala 2.11/g" -i.2.10.bak \ - '{}' \; -find . -name "*.2.10.bak" -exec rm -f {} \; diff --git a/scripts/move_to_spark_1.sh b/scripts/move_to_spark_1.sh deleted file mode 100755 index e20b865..0000000 --- a/scripts/move_to_spark_1.sh +++ /dev/null @@ -1,17 +0,0 @@ -#!/bin/bash - -set +x - -grep -q "spark2" pom.xml -if [[ $? == 1 ]]; -then - echo "POM is already set up for Spark 1 (Spark 1/2 artifacts are missing -spark2 suffix in artifact names)." - echo "Cowardly refusing to move to Spark 1 a second time..." - - exit 1 -fi - -find . -name "pom.xml" -exec sed \ - -e "s/-spark2//g" \ - -e "/spark.version/ s/2.1.0/1.6.3/g" \ - -i.spark1.bak '{}' \; diff --git a/scripts/release/release.sh b/scripts/release/release.sh index 8632f33..8b1dc18 100755 --- a/scripts/release/release.sh +++ b/scripts/release/release.sh @@ -24,64 +24,6 @@ echo "releasing from ${commit} on branch ${branch}" git push origin ${branch} -# do scala 2.10 release -git checkout -b maint_2.10-${release} ${branch} -mvn --batch-mode \ - -P distribution \ - -Dresume=false \ - -Dtag=cannoli-parent_2.10-${release} \ - -DreleaseVersion=${release} \ - -DdevelopmentVersion=${devel} \ - -DbranchName=cannoli_2.10-${release} \ - release:clean \ - release:prepare \ - release:perform - -if [ $? != 0 ]; then - echo "Releasing Spark 1, Scala 2.10 version failed." - exit 1 -fi - -# do scala 2.11 release -git checkout -b maint_2.11-${release} ${branch} -./scripts/move_to_scala_2.11.sh -git commit -a -m "Modifying pom.xml files for Spark 1, Scala 2.11 release." -mvn --batch-mode \ - -P distribution \ - -Dresume=false \ - -Dtag=cannoli-parent_2.11-${release} \ - -DreleaseVersion=${release} \ - -DdevelopmentVersion=${devel} \ - -DbranchName=cannoli_2.11-${release} \ - release:clean \ - release:prepare \ - release:perform - -if [ $? != 0 ]; then - echo "Releasing Spark 1, Scala 2.11 version failed." - exit 1 -fi - -# do spark 2, scala 2.10 release -git checkout -b maint_spark2_2.10-${release} ${branch} -./scripts/move_to_spark_2.sh -git commit -a -m "Modifying pom.xml files for Spark 2, Scala 2.10 release." -mvn --batch-mode \ - -P distribution \ - -Dresume=false \ - -Dtag=cannoli-parent-spark2_2.10-${release} \ - -DreleaseVersion=${release} \ - -DdevelopmentVersion=${devel} \ - -DbranchName=cannoli-spark2_2.10-${release} \ - release:clean \ - release:prepare \ - release:perform - -if [ $? != 0 ]; then - echo "Releasing Spark 2, Scala 2.10 version failed." - exit 1 -fi - # do spark 2, scala 2.11 release git checkout -b maint_spark2_2.11-${release} ${branch} ./scripts/move_to_spark_2.sh